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- PDB-5yz9: zinc finger domain of METTL3-METTL14 N6-methyladenosine methyltra... -

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Basic information

Entry
Database: PDB / ID: 5yz9
Titlezinc finger domain of METTL3-METTL14 N6-methyladenosine methyltransferase
ComponentsN6-adenosine-methyltransferase catalytic subunit
KeywordsRNA BINDING PROTEIN / rna binding / zinc finger / N6-methyladenosine methyltransferase
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / dosage compensation by inactivation of X chromosome / primary miRNA processing ...mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / dosage compensation by inactivation of X chromosome / primary miRNA processing / forebrain radial glial cell differentiation / oxidoreductase complex / S-adenosyl-L-methionine binding / gliogenesis / mRNA modification / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / negative regulation of type I interferon-mediated signaling pathway / stem cell population maintenance / oogenesis / mRNA destabilization / negative regulation of Notch signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA splicing, via spliceosome / mRNA processing / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / protein heterodimerization activity / innate immune response / mRNA binding / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
N6-adenosine-methyltransferase MT-A70-like / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase (EC 2.1.1.62) family profile. / MT-A70-like / MT-A70 / MT-A70-like family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
N6-adenosine-methyltransferase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsDong, X. / Tang, C. / Gong, Z. / Yin, P. / Huang, J.B.
Funding support China, 6items
OrganizationGrant numberCountry
National Key R&D Program of China2016YFA0501200 China
National Natural Science Foundation of China2015CB910900 China
National Natural Science Foundation of China31770799 China
National Natural Science Foundation of China81573400 China
National Natural Science Foundation of China31400644 China
National Natural Science Foundation of China31400735 China
CitationJournal: Protein Cell / Year: 2019
Title: Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase.
Authors: Huang, J. / Dong, X. / Gong, Z. / Qin, L.Y. / Yang, S. / Zhu, Y.L. / Wang, X. / Zhang, D. / Zou, T. / Yin, P. / Tang, C.
History
DepositionDec 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N6-adenosine-methyltransferase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8843
Polymers11,7531
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 960structures with the lowest energy
RepresentativeModel #15closest to the average

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Components

#1: Protein N6-adenosine-methyltransferase catalytic subunit / Methyltransferase-like protein 3 / hMETTL3 / N6-adenosine-methyltransferase 70 kDa subunit / MT-A70


Mass: 11753.191 Da / Num. of mol.: 1 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CB
141isotropic23D CBCA(CO)NH
151isotropic13D H(CCO)NH
161isotropic23D 1H-15N NOESY
171isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM PBS, 100 mM sodium chloride, 90% H2O/10% D2O
Label: 15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMPBSnatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: condition1 / pH: 6.8 / Pressure: 760 mmHg / Temperature: 303 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 960 / Conformers submitted total number: 25

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